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Notes from May 9 meeting

BioPax/gpml: Stick with current proposal right now (BioPAX_in_GPML)
- Decide how to deal with round-trip later
Pathway conversion
- Thomas started adding sticky edges to metabolic pathways and documented the problems (PathwayConversion)
- Should PV be able to collapse complexes (Thomas) or should the visual style be hard-coded into the GPML (Martijn)? Thomas example: BioPAX_in_GPML
- Maybe use sub-gene viewer to look at data from complex?

Main issues:
- Should we include all species, or just mammalian (rat, mouse, human) and use inferator between?
- How to deal with different pathway content for the same pathway in different species?
- Timing of official release and species content to capture as much as possible of the community
Which species should we support now?
- Bruce wants drosophila, zebrafish, worm, yeast etc added to WP now.
- Suggestion (Martijn): Use diff tool to view human and yeast pathway together, buttons to add all differences from one side to the other (inferator function).
- Suggestion (Bruce): Early September mailing to announce WP (+grant etc). Additional species should be up by that time.
- After mailing, we can try to get WP reviewed in Science (Bruce).
- Add yeast (and maybe drosophila) now, without advertisement.
- Add more species as we get more features working.
- Bruce wants 7 species working by September, so we want to find problems with having multiple species early. Martijn prefers to wait until later this summer because bug fixing is a big issue and very time consuming.
- Arabidopsis pathways by Kam's students may be a good test case (later in the summer).
- Add item on main page about which species will be supported soon and which features will be included.
Adding proper edges to pathways
- Bruce suggests hiring summer students to do this
- General idea is to do the human archive and then inferate to rat and mouse